Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
' length 14271 bytes (13 KB) opened URL == downloaded 13 KB * installing *source* package ŒBiocInstaller¹ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help * DONE (BiocInstaller) The downloaded source packages are in Œ/private/tmp/Rtmp44wF3Y/downloaded_packages¹ Bioconductor version 3.1 (BiocInstaller 1.17.1), ?biocLite for help 'BiocInstaller' changed to version 1.17.1 I couldn't tell how I got my R installation into this seemingly locked state, but maybe there should be a force=TRUE option to useDevel for cases like this. Florian I think you somehow had the release version of BiocInstaller installed in R-devel. But it's difficult to know now Dan This is NOT what you want. You now have Bioc 3.1 on R 3.1, but Bioc 3.1 is intended to run with R-devel (3.2) only. Dan On 04/11/14 20:04, Hervé Pagès hpa...@fredhutch.org wrote: Hi, On 11/02/2014 10:58 PM, Dan Tenenbaum wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Kasper Daniel Hansen kasperdanielhan...@gmail.com Cc: bioc-devel@r-project.org Sent: Sunday, November 2, 2014 9:26:25 PM Subject: Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1 Thanks, I incorrectly thought that I was using the same R version as the Bioc-build machines since the r66923 part matched. Now I realize that this tag is used in all of the newest R builds at http://r.research.att.com/. It's admittedly confusing; Agreed. But the error message issued by useDevel() in the current release adds to the confusion: library(BiocInstaller) Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help useDevel() Error: 'devel' version already in use What about something like: Error: you need R 3.2 to run BioC 'devel' version Thanks, H. the question of whether to use R-devel with Bioc-devel has a different answer every six months, but the answer can always be found here: http://www.bioconductor.org/developers/how-to/useDevel/ Also, when looking at the devel build report, you should probably focus more on the version portion of the R version column than on the SVN revision number. Dan On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: You should not be using R-3.1.2 patched with the current devel version of Bioconductor; use R-devel. Best, Kasper On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi, I can't seem to install devel packages via biocLite() and I wonder if something is broken or if I'm missing something. For example, take GenomeInfoDb which is at 1.3.6 and is passing all checks. The usual code using a fresh R 3.1.2-patched install isn't working as it downloads the latest release version (1.2.2): source(http://bioconductor.org/biocLite.R;) Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help ## Was expecting 3.1 here useDevel() Error: 'devel' version already in use biocLite('GenomeInfoDb') BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.2. Installing package(s) 'GenomeInfoDb' trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/Ge no meInfoDb_1.2.2.tgz' Content type 'application/x-gzip' length 404120 bytes (394 KB) opened URL == downloaded 394 KB The downloaded binary packages are in /var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmpxp29xo/downloa de d_packages sessionInfo() R version 3.1.2 Patched (2014-11-01 r66923) ## Note that it matches the current R version used by the Bioc-devel build machines Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.16.0 colorout_1.0-2 loaded via a namespace (and not attached): [1] tools_3.1.2 For my computer it's not problem because I can download the pkg via svn and install locally. But it breaks my tests in TravisCI which relies on biocLite(). Cheers, Leo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
Hi, On 11/02/2014 10:58 PM, Dan Tenenbaum wrote: - Original Message - From: Leonardo Collado Torres lcoll...@jhu.edu To: Kasper Daniel Hansen kasperdanielhan...@gmail.com Cc: bioc-devel@r-project.org Sent: Sunday, November 2, 2014 9:26:25 PM Subject: Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1 Thanks, I incorrectly thought that I was using the same R version as the Bioc-build machines since the r66923 part matched. Now I realize that this tag is used in all of the newest R builds at http://r.research.att.com/. It's admittedly confusing; Agreed. But the error message issued by useDevel() in the current release adds to the confusion: library(BiocInstaller) Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help useDevel() Error: 'devel' version already in use What about something like: Error: you need R 3.2 to run BioC 'devel' version Thanks, H. the question of whether to use R-devel with Bioc-devel has a different answer every six months, but the answer can always be found here: http://www.bioconductor.org/developers/how-to/useDevel/ Also, when looking at the devel build report, you should probably focus more on the version portion of the R version column than on the SVN revision number. Dan On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: You should not be using R-3.1.2 patched with the current devel version of Bioconductor; use R-devel. Best, Kasper On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi, I can't seem to install devel packages via biocLite() and I wonder if something is broken or if I'm missing something. For example, take GenomeInfoDb which is at 1.3.6 and is passing all checks. The usual code using a fresh R 3.1.2-patched install isn't working as it downloads the latest release version (1.2.2): source(http://bioconductor.org/biocLite.R;) Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help ## Was expecting 3.1 here useDevel() Error: 'devel' version already in use biocLite('GenomeInfoDb') BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.2. Installing package(s) 'GenomeInfoDb' trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz' Content type 'application/x-gzip' length 404120 bytes (394 KB) opened URL == downloaded 394 KB The downloaded binary packages are in /var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmpxp29xo/downloaded_packages sessionInfo() R version 3.1.2 Patched (2014-11-01 r66923) ## Note that it matches the current R version used by the Bioc-devel build machines Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.16.0 colorout_1.0-2 loaded via a namespace (and not attached): [1] tools_3.1.2 For my computer it's not problem because I can download the pkg via svn and install locally. But it breaks my tests in TravisCI which relies on biocLite(). Cheers, Leo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
Hi, I can't seem to install devel packages via biocLite() and I wonder if something is broken or if I'm missing something. For example, take GenomeInfoDb which is at 1.3.6 and is passing all checks. The usual code using a fresh R 3.1.2-patched install isn't working as it downloads the latest release version (1.2.2): source(http://bioconductor.org/biocLite.R;) Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help ## Was expecting 3.1 here useDevel() Error: 'devel' version already in use biocLite('GenomeInfoDb') BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.2. Installing package(s) 'GenomeInfoDb' trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz' Content type 'application/x-gzip' length 404120 bytes (394 KB) opened URL == downloaded 394 KB The downloaded binary packages are in /var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmpxp29xo/downloaded_packages sessionInfo() R version 3.1.2 Patched (2014-11-01 r66923) ## Note that it matches the current R version used by the Bioc-devel build machines Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.16.0 colorout_1.0-2 loaded via a namespace (and not attached): [1] tools_3.1.2 For my computer it's not problem because I can download the pkg via svn and install locally. But it breaks my tests in TravisCI which relies on biocLite(). Cheers, Leo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
You should not be using R-3.1.2 patched with the current devel version of Bioconductor; use R-devel. Best, Kasper On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi, I can't seem to install devel packages via biocLite() and I wonder if something is broken or if I'm missing something. For example, take GenomeInfoDb which is at 1.3.6 and is passing all checks. The usual code using a fresh R 3.1.2-patched install isn't working as it downloads the latest release version (1.2.2): source(http://bioconductor.org/biocLite.R;) Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help ## Was expecting 3.1 here useDevel() Error: 'devel' version already in use biocLite('GenomeInfoDb') BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.2. Installing package(s) 'GenomeInfoDb' trying URL ' http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz ' Content type 'application/x-gzip' length 404120 bytes (394 KB) opened URL == downloaded 394 KB The downloaded binary packages are in /var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmpxp29xo/downloaded_packages sessionInfo() R version 3.1.2 Patched (2014-11-01 r66923) ## Note that it matches the current R version used by the Bioc-devel build machines Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.16.0 colorout_1.0-2 loaded via a namespace (and not attached): [1] tools_3.1.2 For my computer it's not problem because I can download the pkg via svn and install locally. But it breaks my tests in TravisCI which relies on biocLite(). Cheers, Leo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Can't seem to use useDevel(); biocLite() for BioC 3.1
Thanks, I incorrectly thought that I was using the same R version as the Bioc-build machines since the r66923 part matched. Now I realize that this tag is used in all of the newest R builds at http://r.research.att.com/. On Sun, Nov 2, 2014 at 9:57 PM, Kasper Daniel Hansen kasperdanielhan...@gmail.com wrote: You should not be using R-3.1.2 patched with the current devel version of Bioconductor; use R-devel. Best, Kasper On Sun, Nov 2, 2014 at 9:32 PM, Leonardo Collado Torres lcoll...@jhu.edu wrote: Hi, I can't seem to install devel packages via biocLite() and I wonder if something is broken or if I'm missing something. For example, take GenomeInfoDb which is at 1.3.6 and is passing all checks. The usual code using a fresh R 3.1.2-patched install isn't working as it downloads the latest release version (1.2.2): source(http://bioconductor.org/biocLite.R;) Bioconductor version 3.0 (BiocInstaller 1.16.0), ?biocLite for help ## Was expecting 3.1 here useDevel() Error: 'devel' version already in use biocLite('GenomeInfoDb') BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.16.0), R version 3.1.2. Installing package(s) 'GenomeInfoDb' trying URL 'http://bioconductor.org/packages/3.0/bioc/bin/macosx/contrib/3.1/GenomeInfoDb_1.2.2.tgz' Content type 'application/x-gzip' length 404120 bytes (394 KB) opened URL == downloaded 394 KB The downloaded binary packages are in /var/folders/cx/n9s558kx6fb7jf5z_pgszgb8gn/T//Rtmpxp29xo/downloaded_packages sessionInfo() R version 3.1.2 Patched (2014-11-01 r66923) ## Note that it matches the current R version used by the Bioc-devel build machines Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.16.0 colorout_1.0-2 loaded via a namespace (and not attached): [1] tools_3.1.2 For my computer it's not problem because I can download the pkg via svn and install locally. But it breaks my tests in TravisCI which relies on biocLite(). Cheers, Leo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel